Multiple sequence alignment - TraesCS6A01G224100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G224100 chr6A 100.000 2774 0 0 1 2774 421101766 421104539 0.000000e+00 5123.0
1 TraesCS6A01G224100 chr6A 93.043 1150 52 11 663 1808 420973389 420974514 0.000000e+00 1655.0
2 TraesCS6A01G224100 chr6A 90.085 827 54 18 951 1774 421367834 421368635 0.000000e+00 1048.0
3 TraesCS6A01G224100 chr6A 90.680 794 53 11 986 1773 421226047 421226825 0.000000e+00 1037.0
4 TraesCS6A01G224100 chr6A 93.000 100 7 0 1805 1904 420974592 420974691 2.230000e-31 147.0
5 TraesCS6A01G224100 chr6B 91.674 1153 55 16 677 1808 461904004 461902872 0.000000e+00 1559.0
6 TraesCS6A01G224100 chr6B 90.844 1114 52 24 695 1808 461962140 461961077 0.000000e+00 1447.0
7 TraesCS6A01G224100 chr6B 93.462 826 36 11 986 1808 461848278 461847468 0.000000e+00 1210.0
8 TraesCS6A01G224100 chr6B 90.260 308 29 1 2114 2420 461846930 461846623 4.300000e-108 401.0
9 TraesCS6A01G224100 chr6B 92.271 207 11 2 1806 2007 461902803 461902597 3.500000e-74 289.0
10 TraesCS6A01G224100 chr6B 89.130 230 17 4 1806 2027 461847399 461847170 2.100000e-71 279.0
11 TraesCS6A01G224100 chr6B 80.769 364 42 16 175 535 461904425 461904087 2.740000e-65 259.0
12 TraesCS6A01G224100 chr6B 80.114 352 45 12 76 418 461968366 461968031 3.570000e-59 239.0
13 TraesCS6A01G224100 chr6B 88.485 165 14 4 1826 1990 461960966 461960807 7.840000e-46 195.0
14 TraesCS6A01G224100 chr6B 90.099 101 7 3 567 667 461904084 461903987 8.060000e-26 128.0
15 TraesCS6A01G224100 chr6D 90.941 1148 63 15 663 1808 298445119 298444011 0.000000e+00 1506.0
16 TraesCS6A01G224100 chr6D 90.331 1148 46 17 663 1808 298399637 298398553 0.000000e+00 1445.0
17 TraesCS6A01G224100 chr6D 88.199 983 83 20 1805 2772 298398483 298397519 0.000000e+00 1142.0
18 TraesCS6A01G224100 chr6D 91.909 791 43 11 986 1773 298207298 298206526 0.000000e+00 1086.0
19 TraesCS6A01G224100 chr6D 85.882 340 35 10 307 645 298445433 298445106 1.580000e-92 350.0
20 TraesCS6A01G224100 chr6D 88.623 167 11 7 1826 1990 298443935 298443775 2.180000e-46 196.0
21 TraesCS6A01G224100 chr6D 94.059 101 5 1 435 535 298399797 298399698 4.790000e-33 152.0
22 TraesCS6A01G224100 chr6D 90.411 73 4 1 560 629 298399702 298399630 2.940000e-15 93.5
23 TraesCS6A01G224100 chr1A 87.500 88 10 1 2659 2746 470348124 470348038 1.760000e-17 100.0
24 TraesCS6A01G224100 chr7D 100.000 30 0 0 2608 2637 589037205 589037176 3.860000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G224100 chr6A 421101766 421104539 2773 False 5123.000 5123 100.000000 1 2774 1 chr6A.!!$F1 2773
1 TraesCS6A01G224100 chr6A 421367834 421368635 801 False 1048.000 1048 90.085000 951 1774 1 chr6A.!!$F3 823
2 TraesCS6A01G224100 chr6A 421226047 421226825 778 False 1037.000 1037 90.680000 986 1773 1 chr6A.!!$F2 787
3 TraesCS6A01G224100 chr6A 420973389 420974691 1302 False 901.000 1655 93.021500 663 1904 2 chr6A.!!$F4 1241
4 TraesCS6A01G224100 chr6B 461960807 461962140 1333 True 821.000 1447 89.664500 695 1990 2 chr6B.!!$R4 1295
5 TraesCS6A01G224100 chr6B 461846623 461848278 1655 True 630.000 1210 90.950667 986 2420 3 chr6B.!!$R2 1434
6 TraesCS6A01G224100 chr6B 461902597 461904425 1828 True 558.750 1559 88.703250 175 2007 4 chr6B.!!$R3 1832
7 TraesCS6A01G224100 chr6D 298206526 298207298 772 True 1086.000 1086 91.909000 986 1773 1 chr6D.!!$R1 787
8 TraesCS6A01G224100 chr6D 298397519 298399797 2278 True 708.125 1445 90.750000 435 2772 4 chr6D.!!$R2 2337
9 TraesCS6A01G224100 chr6D 298443775 298445433 1658 True 684.000 1506 88.482000 307 1990 3 chr6D.!!$R3 1683

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
427 428 0.103208 CTAAGCACGCCCACTCCTAG 59.897 60.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 2825 0.037605 ACCAGTGCTACGGTGCTAAC 60.038 55.0 3.74 0.0 33.05 2.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.500125 GTGGATGGAAGGAGGGGA 57.500 61.111 0.00 0.00 0.00 4.81
18 19 2.225792 GTGGATGGAAGGAGGGGAG 58.774 63.158 0.00 0.00 0.00 4.30
19 20 1.004758 TGGATGGAAGGAGGGGAGG 59.995 63.158 0.00 0.00 0.00 4.30
20 21 2.456443 GGATGGAAGGAGGGGAGGC 61.456 68.421 0.00 0.00 0.00 4.70
21 22 1.694169 GATGGAAGGAGGGGAGGCA 60.694 63.158 0.00 0.00 0.00 4.75
22 23 1.988982 GATGGAAGGAGGGGAGGCAC 61.989 65.000 0.00 0.00 0.00 5.01
23 24 2.610859 GGAAGGAGGGGAGGCACA 60.611 66.667 0.00 0.00 0.00 4.57
24 25 2.003548 GGAAGGAGGGGAGGCACAT 61.004 63.158 0.00 0.00 0.00 3.21
25 26 1.529309 GAAGGAGGGGAGGCACATC 59.471 63.158 0.00 0.00 0.00 3.06
26 27 1.229951 AAGGAGGGGAGGCACATCA 60.230 57.895 0.00 0.00 0.00 3.07
27 28 0.625683 AAGGAGGGGAGGCACATCAT 60.626 55.000 0.00 0.00 0.00 2.45
28 29 1.059006 AGGAGGGGAGGCACATCATC 61.059 60.000 0.00 0.00 0.00 2.92
29 30 1.059006 GGAGGGGAGGCACATCATCT 61.059 60.000 0.00 0.00 0.00 2.90
30 31 0.396060 GAGGGGAGGCACATCATCTC 59.604 60.000 0.00 0.00 0.00 2.75
31 32 1.070445 GGGGAGGCACATCATCTCG 59.930 63.158 0.00 0.00 0.00 4.04
32 33 1.596477 GGGAGGCACATCATCTCGC 60.596 63.158 0.00 0.00 34.31 5.03
33 34 1.596477 GGAGGCACATCATCTCGCC 60.596 63.158 0.00 0.00 45.23 5.54
35 36 3.728474 GGCACATCATCTCGCCAG 58.272 61.111 0.00 0.00 44.25 4.85
36 37 1.144716 GGCACATCATCTCGCCAGA 59.855 57.895 0.00 0.00 44.25 3.86
37 38 0.879400 GGCACATCATCTCGCCAGAG 60.879 60.000 0.00 0.00 44.25 3.35
46 47 4.988744 TCGCCAGAGAGGAGGTAG 57.011 61.111 0.00 0.00 41.22 3.18
47 48 2.308185 TCGCCAGAGAGGAGGTAGA 58.692 57.895 0.00 0.00 41.22 2.59
48 49 0.847373 TCGCCAGAGAGGAGGTAGAT 59.153 55.000 0.00 0.00 41.22 1.98
49 50 1.202830 TCGCCAGAGAGGAGGTAGATC 60.203 57.143 0.00 0.00 41.22 2.75
50 51 1.243902 GCCAGAGAGGAGGTAGATCG 58.756 60.000 0.00 0.00 41.22 3.69
51 52 1.904287 CCAGAGAGGAGGTAGATCGG 58.096 60.000 0.00 0.00 41.22 4.18
52 53 1.243902 CAGAGAGGAGGTAGATCGGC 58.756 60.000 0.00 0.00 0.00 5.54
53 54 0.847373 AGAGAGGAGGTAGATCGGCA 59.153 55.000 0.00 0.00 0.00 5.69
54 55 0.955905 GAGAGGAGGTAGATCGGCAC 59.044 60.000 0.00 0.00 0.00 5.01
55 56 0.553819 AGAGGAGGTAGATCGGCACT 59.446 55.000 0.00 0.00 0.00 4.40
56 57 0.671251 GAGGAGGTAGATCGGCACTG 59.329 60.000 0.00 0.00 0.00 3.66
57 58 0.259065 AGGAGGTAGATCGGCACTGA 59.741 55.000 0.00 0.00 0.00 3.41
58 59 0.386113 GGAGGTAGATCGGCACTGAC 59.614 60.000 0.00 0.00 0.00 3.51
59 60 1.103803 GAGGTAGATCGGCACTGACA 58.896 55.000 0.00 0.00 0.00 3.58
60 61 0.818296 AGGTAGATCGGCACTGACAC 59.182 55.000 0.00 0.00 0.00 3.67
61 62 0.818296 GGTAGATCGGCACTGACACT 59.182 55.000 0.00 0.00 0.00 3.55
62 63 2.022195 GGTAGATCGGCACTGACACTA 58.978 52.381 0.00 0.00 0.00 2.74
63 64 2.223525 GGTAGATCGGCACTGACACTAC 60.224 54.545 13.03 13.03 33.86 2.73
64 65 0.818296 AGATCGGCACTGACACTACC 59.182 55.000 0.00 0.00 0.00 3.18
65 66 0.818296 GATCGGCACTGACACTACCT 59.182 55.000 0.00 0.00 0.00 3.08
66 67 0.818296 ATCGGCACTGACACTACCTC 59.182 55.000 0.00 0.00 0.00 3.85
67 68 1.215647 CGGCACTGACACTACCTCC 59.784 63.158 0.00 0.00 0.00 4.30
68 69 1.215647 GGCACTGACACTACCTCCG 59.784 63.158 0.00 0.00 0.00 4.63
69 70 1.533469 GGCACTGACACTACCTCCGT 61.533 60.000 0.00 0.00 0.00 4.69
70 71 0.388649 GCACTGACACTACCTCCGTG 60.389 60.000 0.00 0.00 38.32 4.94
71 72 0.243907 CACTGACACTACCTCCGTGG 59.756 60.000 0.00 0.00 42.93 4.94
72 73 0.898789 ACTGACACTACCTCCGTGGG 60.899 60.000 0.00 0.00 41.11 4.61
73 74 0.611062 CTGACACTACCTCCGTGGGA 60.611 60.000 0.00 0.00 41.11 4.37
81 82 4.075793 CTCCGTGGGAGGGAGGGA 62.076 72.222 3.68 0.00 45.43 4.20
82 83 4.075793 TCCGTGGGAGGGAGGGAG 62.076 72.222 0.00 0.00 0.00 4.30
84 85 4.075793 CGTGGGAGGGAGGGAGGA 62.076 72.222 0.00 0.00 0.00 3.71
85 86 2.454941 GTGGGAGGGAGGGAGGAA 59.545 66.667 0.00 0.00 0.00 3.36
86 87 1.690985 GTGGGAGGGAGGGAGGAAG 60.691 68.421 0.00 0.00 0.00 3.46
87 88 2.040359 GGGAGGGAGGGAGGAAGG 60.040 72.222 0.00 0.00 0.00 3.46
88 89 2.647949 GGGAGGGAGGGAGGAAGGA 61.648 68.421 0.00 0.00 0.00 3.36
89 90 1.396594 GGAGGGAGGGAGGAAGGAA 59.603 63.158 0.00 0.00 0.00 3.36
90 91 0.692756 GGAGGGAGGGAGGAAGGAAG 60.693 65.000 0.00 0.00 0.00 3.46
91 92 0.340208 GAGGGAGGGAGGAAGGAAGA 59.660 60.000 0.00 0.00 0.00 2.87
92 93 0.800239 AGGGAGGGAGGAAGGAAGAA 59.200 55.000 0.00 0.00 0.00 2.52
93 94 1.154434 AGGGAGGGAGGAAGGAAGAAA 59.846 52.381 0.00 0.00 0.00 2.52
94 95 1.993301 GGGAGGGAGGAAGGAAGAAAA 59.007 52.381 0.00 0.00 0.00 2.29
95 96 2.291024 GGGAGGGAGGAAGGAAGAAAAC 60.291 54.545 0.00 0.00 0.00 2.43
96 97 2.615747 GGAGGGAGGAAGGAAGAAAACG 60.616 54.545 0.00 0.00 0.00 3.60
97 98 2.038689 GAGGGAGGAAGGAAGAAAACGT 59.961 50.000 0.00 0.00 0.00 3.99
98 99 2.442126 AGGGAGGAAGGAAGAAAACGTT 59.558 45.455 0.00 0.00 0.00 3.99
99 100 3.117625 AGGGAGGAAGGAAGAAAACGTTT 60.118 43.478 7.96 7.96 0.00 3.60
100 101 4.103627 AGGGAGGAAGGAAGAAAACGTTTA 59.896 41.667 15.03 0.00 0.00 2.01
101 102 4.454847 GGGAGGAAGGAAGAAAACGTTTAG 59.545 45.833 15.03 0.00 0.00 1.85
102 103 4.454847 GGAGGAAGGAAGAAAACGTTTAGG 59.545 45.833 15.03 0.00 0.00 2.69
103 104 5.300411 AGGAAGGAAGAAAACGTTTAGGA 57.700 39.130 15.03 0.00 0.00 2.94
104 105 5.061853 AGGAAGGAAGAAAACGTTTAGGAC 58.938 41.667 15.03 6.79 0.00 3.85
118 119 4.669318 GTTTAGGACGATCGATCAAGTGA 58.331 43.478 24.34 4.37 0.00 3.41
119 120 5.282510 GTTTAGGACGATCGATCAAGTGAT 58.717 41.667 24.34 7.93 37.51 3.06
120 121 3.634568 AGGACGATCGATCAAGTGATC 57.365 47.619 24.34 10.69 45.60 2.92
121 122 3.218453 AGGACGATCGATCAAGTGATCT 58.782 45.455 24.34 8.89 46.58 2.75
122 123 3.252215 AGGACGATCGATCAAGTGATCTC 59.748 47.826 24.34 3.65 46.58 2.75
123 124 3.252215 GGACGATCGATCAAGTGATCTCT 59.748 47.826 24.34 6.08 46.58 3.10
124 125 4.463209 GACGATCGATCAAGTGATCTCTC 58.537 47.826 24.34 12.41 46.58 3.20
125 126 3.879892 ACGATCGATCAAGTGATCTCTCA 59.120 43.478 24.34 1.91 46.58 3.27
126 127 4.336713 ACGATCGATCAAGTGATCTCTCAA 59.663 41.667 24.34 1.29 46.58 3.02
127 128 5.163612 ACGATCGATCAAGTGATCTCTCAAA 60.164 40.000 24.34 0.00 46.58 2.69
128 129 5.172951 CGATCGATCAAGTGATCTCTCAAAC 59.827 44.000 24.40 0.00 46.58 2.93
129 130 5.391312 TCGATCAAGTGATCTCTCAAACA 57.609 39.130 17.03 0.00 46.58 2.83
130 131 5.164233 TCGATCAAGTGATCTCTCAAACAC 58.836 41.667 17.03 0.00 46.58 3.32
131 132 4.925646 CGATCAAGTGATCTCTCAAACACA 59.074 41.667 17.03 0.00 46.58 3.72
132 133 5.406477 CGATCAAGTGATCTCTCAAACACAA 59.594 40.000 17.03 0.00 46.58 3.33
133 134 6.073602 CGATCAAGTGATCTCTCAAACACAAA 60.074 38.462 17.03 0.00 46.58 2.83
134 135 6.363577 TCAAGTGATCTCTCAAACACAAAC 57.636 37.500 0.00 0.00 35.97 2.93
135 136 5.879777 TCAAGTGATCTCTCAAACACAAACA 59.120 36.000 0.00 0.00 35.97 2.83
136 137 5.741388 AGTGATCTCTCAAACACAAACAC 57.259 39.130 0.00 0.00 35.97 3.32
137 138 5.431765 AGTGATCTCTCAAACACAAACACT 58.568 37.500 0.00 0.00 35.97 3.55
138 139 5.882557 AGTGATCTCTCAAACACAAACACTT 59.117 36.000 0.00 0.00 35.97 3.16
139 140 6.037610 AGTGATCTCTCAAACACAAACACTTC 59.962 38.462 0.00 0.00 35.97 3.01
140 141 5.296780 TGATCTCTCAAACACAAACACTTCC 59.703 40.000 0.00 0.00 0.00 3.46
141 142 4.584874 TCTCTCAAACACAAACACTTCCA 58.415 39.130 0.00 0.00 0.00 3.53
142 143 5.007034 TCTCTCAAACACAAACACTTCCAA 58.993 37.500 0.00 0.00 0.00 3.53
143 144 5.123820 TCTCTCAAACACAAACACTTCCAAG 59.876 40.000 0.00 0.00 0.00 3.61
144 145 4.157656 TCTCAAACACAAACACTTCCAAGG 59.842 41.667 0.00 0.00 0.00 3.61
145 146 3.194542 TCAAACACAAACACTTCCAAGGG 59.805 43.478 0.00 0.00 34.93 3.95
146 147 1.775385 ACACAAACACTTCCAAGGGG 58.225 50.000 0.00 0.00 32.35 4.79
147 148 1.006639 ACACAAACACTTCCAAGGGGT 59.993 47.619 0.00 0.00 32.35 4.95
148 149 2.242708 ACACAAACACTTCCAAGGGGTA 59.757 45.455 0.00 0.00 32.35 3.69
149 150 3.117284 ACACAAACACTTCCAAGGGGTAT 60.117 43.478 0.00 0.00 32.35 2.73
150 151 4.105057 ACACAAACACTTCCAAGGGGTATA 59.895 41.667 0.00 0.00 32.35 1.47
151 152 5.074115 CACAAACACTTCCAAGGGGTATAA 58.926 41.667 0.00 0.00 32.35 0.98
152 153 5.536916 CACAAACACTTCCAAGGGGTATAAA 59.463 40.000 0.00 0.00 32.35 1.40
153 154 5.773176 ACAAACACTTCCAAGGGGTATAAAG 59.227 40.000 0.00 0.00 32.35 1.85
154 155 4.586306 ACACTTCCAAGGGGTATAAAGG 57.414 45.455 0.00 0.00 32.35 3.11
155 156 3.920841 ACACTTCCAAGGGGTATAAAGGT 59.079 43.478 0.00 0.00 32.35 3.50
156 157 5.102967 ACACTTCCAAGGGGTATAAAGGTA 58.897 41.667 0.00 0.00 32.35 3.08
157 158 5.734634 ACACTTCCAAGGGGTATAAAGGTAT 59.265 40.000 0.00 0.00 32.35 2.73
158 159 6.062095 CACTTCCAAGGGGTATAAAGGTATG 58.938 44.000 0.00 0.00 34.93 2.39
159 160 5.974370 ACTTCCAAGGGGTATAAAGGTATGA 59.026 40.000 0.00 0.00 34.93 2.15
160 161 6.624021 ACTTCCAAGGGGTATAAAGGTATGAT 59.376 38.462 0.00 0.00 34.93 2.45
161 162 7.130442 ACTTCCAAGGGGTATAAAGGTATGATT 59.870 37.037 0.00 0.00 34.93 2.57
162 163 7.474474 TCCAAGGGGTATAAAGGTATGATTT 57.526 36.000 0.00 0.00 34.93 2.17
163 164 7.889178 TCCAAGGGGTATAAAGGTATGATTTT 58.111 34.615 0.00 0.00 34.93 1.82
164 165 8.348354 TCCAAGGGGTATAAAGGTATGATTTTT 58.652 33.333 0.00 0.00 34.93 1.94
165 166 8.638873 CCAAGGGGTATAAAGGTATGATTTTTC 58.361 37.037 0.00 0.00 0.00 2.29
166 167 9.196139 CAAGGGGTATAAAGGTATGATTTTTCA 57.804 33.333 0.00 0.00 0.00 2.69
167 168 8.996651 AGGGGTATAAAGGTATGATTTTTCAG 57.003 34.615 0.00 0.00 0.00 3.02
168 169 8.004801 AGGGGTATAAAGGTATGATTTTTCAGG 58.995 37.037 0.00 0.00 0.00 3.86
169 170 8.002459 GGGGTATAAAGGTATGATTTTTCAGGA 58.998 37.037 0.00 0.00 0.00 3.86
170 171 9.416284 GGGTATAAAGGTATGATTTTTCAGGAA 57.584 33.333 0.00 0.00 0.00 3.36
189 190 9.787532 TTCAGGAATTTTCATATTCTTTAAGCG 57.212 29.630 0.00 0.00 35.37 4.68
197 198 8.492673 TTTCATATTCTTTAAGCGAGATGTGT 57.507 30.769 0.00 0.00 0.00 3.72
199 200 7.264947 TCATATTCTTTAAGCGAGATGTGTCA 58.735 34.615 0.00 0.00 0.00 3.58
208 209 9.841880 TTTAAGCGAGATGTGTCAGTATATATC 57.158 33.333 0.00 0.00 0.00 1.63
209 210 7.454260 AAGCGAGATGTGTCAGTATATATCA 57.546 36.000 0.00 0.00 0.00 2.15
211 212 6.431234 AGCGAGATGTGTCAGTATATATCACA 59.569 38.462 6.64 6.64 41.93 3.58
218 219 9.649167 ATGTGTCAGTATATATCACATCACATG 57.351 33.333 17.12 0.00 43.28 3.21
296 297 9.938280 ATAAGTGCTAGTACAATACTGTTTTGA 57.062 29.630 16.18 0.00 39.81 2.69
297 298 8.848474 AAGTGCTAGTACAATACTGTTTTGAT 57.152 30.769 16.18 5.90 39.81 2.57
298 299 9.938280 AAGTGCTAGTACAATACTGTTTTGATA 57.062 29.630 16.18 6.58 39.81 2.15
299 300 9.587772 AGTGCTAGTACAATACTGTTTTGATAG 57.412 33.333 16.18 14.16 39.81 2.08
300 301 9.582431 GTGCTAGTACAATACTGTTTTGATAGA 57.418 33.333 16.18 0.88 39.81 1.98
301 302 9.582431 TGCTAGTACAATACTGTTTTGATAGAC 57.418 33.333 16.18 8.97 39.81 2.59
302 303 9.804758 GCTAGTACAATACTGTTTTGATAGACT 57.195 33.333 16.18 13.99 39.81 3.24
305 306 9.640963 AGTACAATACTGTTTTGATAGACTCAC 57.359 33.333 16.18 3.32 37.69 3.51
337 338 3.686726 CAGTTTACTCAAGGATGGCTGTC 59.313 47.826 0.00 0.00 0.00 3.51
343 344 1.376424 AAGGATGGCTGTCGTGCTG 60.376 57.895 0.00 0.00 33.16 4.41
346 347 2.359107 ATGGCTGTCGTGCTGGTG 60.359 61.111 0.00 0.00 0.00 4.17
390 391 6.893554 TCTGATTGAGAATCCCATTGATGTTT 59.106 34.615 0.00 0.00 37.09 2.83
391 392 7.398047 TCTGATTGAGAATCCCATTGATGTTTT 59.602 33.333 0.00 0.00 37.09 2.43
392 393 7.909518 TGATTGAGAATCCCATTGATGTTTTT 58.090 30.769 0.00 0.00 37.09 1.94
413 414 2.138596 TTGTTGCTGCAAAGCTAAGC 57.861 45.000 17.80 3.26 37.46 3.09
426 427 1.956629 GCTAAGCACGCCCACTCCTA 61.957 60.000 0.00 0.00 0.00 2.94
427 428 0.103208 CTAAGCACGCCCACTCCTAG 59.897 60.000 0.00 0.00 0.00 3.02
433 434 1.258445 ACGCCCACTCCTAGGACAAG 61.258 60.000 7.62 0.44 0.00 3.16
440 442 3.807309 TCCTAGGACAAGGAGGCAA 57.193 52.632 7.62 0.00 40.86 4.52
448 450 1.876156 GACAAGGAGGCAACAGTTCAG 59.124 52.381 0.00 0.00 41.41 3.02
477 479 1.003580 TCAGAGAGAACAATGCCACCC 59.996 52.381 0.00 0.00 0.00 4.61
530 554 8.474831 GTTTTAAAATGGGCACAGGAGTATATT 58.525 33.333 3.52 0.00 0.00 1.28
531 555 9.702253 TTTTAAAATGGGCACAGGAGTATATTA 57.298 29.630 0.00 0.00 0.00 0.98
532 556 8.918202 TTAAAATGGGCACAGGAGTATATTAG 57.082 34.615 0.00 0.00 0.00 1.73
533 557 6.515512 AAATGGGCACAGGAGTATATTAGT 57.484 37.500 0.00 0.00 0.00 2.24
534 558 7.626999 AAATGGGCACAGGAGTATATTAGTA 57.373 36.000 0.00 0.00 0.00 1.82
535 559 6.859112 ATGGGCACAGGAGTATATTAGTAG 57.141 41.667 0.00 0.00 0.00 2.57
536 560 5.712752 TGGGCACAGGAGTATATTAGTAGT 58.287 41.667 0.00 0.00 0.00 2.73
537 561 6.855667 TGGGCACAGGAGTATATTAGTAGTA 58.144 40.000 0.00 0.00 0.00 1.82
538 562 6.946583 TGGGCACAGGAGTATATTAGTAGTAG 59.053 42.308 0.00 0.00 0.00 2.57
539 563 6.127675 GGGCACAGGAGTATATTAGTAGTAGC 60.128 46.154 0.00 0.00 0.00 3.58
540 564 6.660094 GGCACAGGAGTATATTAGTAGTAGCT 59.340 42.308 0.00 0.00 0.00 3.32
541 565 7.177041 GGCACAGGAGTATATTAGTAGTAGCTT 59.823 40.741 0.00 0.00 0.00 3.74
542 566 8.578151 GCACAGGAGTATATTAGTAGTAGCTTT 58.422 37.037 0.00 0.00 0.00 3.51
637 664 3.012518 GACTCCATCCAATTCCACACAG 58.987 50.000 0.00 0.00 0.00 3.66
641 668 3.843619 TCCATCCAATTCCACACAGTAGA 59.156 43.478 0.00 0.00 0.00 2.59
642 669 4.288366 TCCATCCAATTCCACACAGTAGAA 59.712 41.667 0.00 0.00 0.00 2.10
643 670 5.009631 CCATCCAATTCCACACAGTAGAAA 58.990 41.667 0.00 0.00 0.00 2.52
644 671 5.476599 CCATCCAATTCCACACAGTAGAAAA 59.523 40.000 0.00 0.00 0.00 2.29
645 672 6.015519 CCATCCAATTCCACACAGTAGAAAAA 60.016 38.462 0.00 0.00 0.00 1.94
664 691 5.596836 AAAAAGAACCAAGTGCTGATCAA 57.403 34.783 0.00 0.00 0.00 2.57
665 692 5.596836 AAAAGAACCAAGTGCTGATCAAA 57.403 34.783 0.00 0.00 0.00 2.69
666 693 5.596836 AAAGAACCAAGTGCTGATCAAAA 57.403 34.783 0.00 0.00 0.00 2.44
667 694 5.596836 AAGAACCAAGTGCTGATCAAAAA 57.403 34.783 0.00 0.00 0.00 1.94
692 719 4.391405 AAAAAGAACAAGTGGGAGCAAG 57.609 40.909 0.00 0.00 0.00 4.01
693 720 1.322442 AAGAACAAGTGGGAGCAAGC 58.678 50.000 0.00 0.00 0.00 4.01
806 833 1.209128 CGTTTTGCTGTCTGTCGACT 58.791 50.000 17.92 0.00 40.86 4.18
861 888 2.165167 CCACACACCATCATCAGCTTT 58.835 47.619 0.00 0.00 0.00 3.51
866 893 2.575279 ACACCATCATCAGCTTTCTCCT 59.425 45.455 0.00 0.00 0.00 3.69
886 913 2.066999 GCATCCGACTCCCTCCCTT 61.067 63.158 0.00 0.00 0.00 3.95
906 966 2.046314 CCCCGACCCATCACACAC 60.046 66.667 0.00 0.00 0.00 3.82
907 967 2.747022 CCCGACCCATCACACACA 59.253 61.111 0.00 0.00 0.00 3.72
908 968 1.671054 CCCGACCCATCACACACAC 60.671 63.158 0.00 0.00 0.00 3.82
909 969 1.070615 CCGACCCATCACACACACA 59.929 57.895 0.00 0.00 0.00 3.72
910 970 1.227999 CCGACCCATCACACACACAC 61.228 60.000 0.00 0.00 0.00 3.82
911 971 0.531753 CGACCCATCACACACACACA 60.532 55.000 0.00 0.00 0.00 3.72
912 972 0.944386 GACCCATCACACACACACAC 59.056 55.000 0.00 0.00 0.00 3.82
913 973 0.254462 ACCCATCACACACACACACA 59.746 50.000 0.00 0.00 0.00 3.72
914 974 0.662619 CCCATCACACACACACACAC 59.337 55.000 0.00 0.00 0.00 3.82
915 975 1.377536 CCATCACACACACACACACA 58.622 50.000 0.00 0.00 0.00 3.72
916 976 1.063912 CCATCACACACACACACACAC 59.936 52.381 0.00 0.00 0.00 3.82
1004 1079 2.163010 CAGAGTAAGCAACAGCAATGGG 59.837 50.000 0.00 0.00 0.00 4.00
1213 1288 4.626081 AGCGCGGCAACTTCACCT 62.626 61.111 8.83 0.00 0.00 4.00
1215 1290 2.972505 CGCGGCAACTTCACCTGT 60.973 61.111 0.00 0.00 0.00 4.00
1252 1327 0.392863 CATCCAACTCCACGCCATGA 60.393 55.000 0.00 0.00 0.00 3.07
1500 1581 4.498520 ATGTCGCCGGAGCAGTCG 62.499 66.667 5.05 0.00 39.83 4.18
1575 1674 0.458260 GAAGCTCTTCCTCGGAGTCC 59.542 60.000 0.00 0.00 33.64 3.85
1683 1782 0.669077 CCTTCGGCGTAGATAGTGCT 59.331 55.000 15.43 0.00 0.00 4.40
1687 1786 0.306840 CGGCGTAGATAGTGCTTCGA 59.693 55.000 0.00 0.00 31.44 3.71
1688 1787 1.756367 GGCGTAGATAGTGCTTCGAC 58.244 55.000 0.00 0.00 31.44 4.20
1689 1788 1.386961 GCGTAGATAGTGCTTCGACG 58.613 55.000 0.00 2.62 42.63 5.12
1690 1789 1.267932 GCGTAGATAGTGCTTCGACGT 60.268 52.381 7.85 0.00 42.03 4.34
1753 1852 3.740631 TCATGCAGGCTAGTGACATAG 57.259 47.619 0.00 0.00 0.00 2.23
1816 1996 4.218417 GCTATGTTCATATTTTGGCCGGAT 59.782 41.667 5.05 0.00 0.00 4.18
1834 2040 3.668757 CGGATGTTTCTGTAGTTCGTCGA 60.669 47.826 0.00 0.00 0.00 4.20
2016 2228 7.169140 GGTTCATATTGCGAAAAGTCTGTTTTT 59.831 33.333 0.00 0.00 33.19 1.94
2060 2276 5.603596 TCTTCGTTGCTCCTTTAGTTGTAA 58.396 37.500 0.00 0.00 0.00 2.41
2098 2314 1.070309 GCTGCTAAGAAATCATCCGCG 60.070 52.381 0.00 0.00 0.00 6.46
2107 2323 3.670637 ATCATCCGCGTGCACAGCT 62.671 57.895 24.04 9.22 0.00 4.24
2120 2520 1.679305 ACAGCTGTCCGATCCGTCT 60.679 57.895 15.25 0.00 0.00 4.18
2236 2636 2.434843 CGTAGCATGCCTCCCTCCA 61.435 63.158 15.66 0.00 0.00 3.86
2240 2640 2.673200 GCATGCCTCCCTCCAGTCA 61.673 63.158 6.36 0.00 0.00 3.41
2244 2644 2.452114 CCTCCCTCCAGTCACCCT 59.548 66.667 0.00 0.00 0.00 4.34
2250 2650 2.447572 TCCAGTCACCCTGCACCA 60.448 61.111 0.00 0.00 40.06 4.17
2272 2672 2.263077 CGTTGTTCTACTAGCCAGCAG 58.737 52.381 0.00 0.00 0.00 4.24
2287 2687 1.153568 GCAGCATCGTAGCACCTCA 60.154 57.895 4.81 0.00 36.85 3.86
2315 2716 0.318614 GTTGCAACATGGTTGGTCGG 60.319 55.000 24.52 0.00 0.00 4.79
2401 2802 1.807573 CTTGAAGCGTCGGGAGCTC 60.808 63.158 4.71 4.71 45.31 4.09
2407 2808 2.185350 CGTCGGGAGCTCTGCATT 59.815 61.111 14.64 0.00 0.00 3.56
2420 2821 2.352821 TGCATTGCAGCCCCATCAC 61.353 57.895 7.38 0.00 33.32 3.06
2421 2822 2.802792 CATTGCAGCCCCATCACG 59.197 61.111 0.00 0.00 0.00 4.35
2423 2824 1.452651 ATTGCAGCCCCATCACGAG 60.453 57.895 0.00 0.00 0.00 4.18
2424 2825 2.898920 ATTGCAGCCCCATCACGAGG 62.899 60.000 0.00 0.00 0.00 4.63
2425 2826 4.101448 GCAGCCCCATCACGAGGT 62.101 66.667 0.00 0.00 0.00 3.85
2426 2827 2.671070 CAGCCCCATCACGAGGTT 59.329 61.111 0.00 0.00 0.00 3.50
2427 2828 1.904771 CAGCCCCATCACGAGGTTA 59.095 57.895 0.00 0.00 0.00 2.85
2429 2830 1.523938 GCCCCATCACGAGGTTAGC 60.524 63.158 0.00 0.00 0.00 3.09
2430 2831 1.904771 CCCCATCACGAGGTTAGCA 59.095 57.895 0.00 0.00 0.00 3.49
2431 2832 0.462047 CCCCATCACGAGGTTAGCAC 60.462 60.000 0.00 0.00 0.00 4.40
2432 2833 0.462047 CCCATCACGAGGTTAGCACC 60.462 60.000 0.00 0.00 44.67 5.01
2460 2861 3.075005 TGCTCCCCTACAGGTCGC 61.075 66.667 0.00 0.00 0.00 5.19
2461 2862 4.208686 GCTCCCCTACAGGTCGCG 62.209 72.222 0.00 0.00 0.00 5.87
2462 2863 4.208686 CTCCCCTACAGGTCGCGC 62.209 72.222 0.00 0.00 0.00 6.86
2483 2884 1.019673 CCCATCCATCTTGAAGCACG 58.980 55.000 0.00 0.00 0.00 5.34
2485 2886 1.938577 CCATCCATCTTGAAGCACGAG 59.061 52.381 0.00 0.00 0.00 4.18
2534 2936 3.116091 AGGTGTGCCCTTTCTTGTG 57.884 52.632 0.00 0.00 42.73 3.33
2537 2939 1.109323 GTGTGCCCTTTCTTGTGGCT 61.109 55.000 0.00 0.00 45.56 4.75
2547 2949 2.599281 TTGTGGCTCTCCGTCCGA 60.599 61.111 0.00 0.00 34.14 4.55
2556 2958 4.717629 TCCGTCCGACTTGCAGCG 62.718 66.667 0.00 0.00 0.00 5.18
2579 2982 3.050275 GCTGGGGAGCGTTGTGTC 61.050 66.667 0.00 0.00 0.00 3.67
2619 3022 2.726274 GCATGGCATAGCAGCACC 59.274 61.111 14.33 0.00 35.83 5.01
2643 3046 0.678950 CAACAACCATCCCGGCTTTT 59.321 50.000 0.00 0.00 39.03 2.27
2648 3051 0.696501 ACCATCCCGGCTTTTACACT 59.303 50.000 0.00 0.00 39.03 3.55
2650 3053 1.094785 CATCCCGGCTTTTACACTGG 58.905 55.000 0.00 0.00 0.00 4.00
2655 3058 1.802365 CCGGCTTTTACACTGGTGTAC 59.198 52.381 12.40 2.68 44.81 2.90
2707 3110 5.034200 TGGGCCTCCAAGTATAGAGTTTTA 58.966 41.667 4.53 0.00 40.73 1.52
2761 3164 9.918630 GGATGACCTAAAATTTATCAATCCATG 57.081 33.333 0.00 0.00 0.00 3.66
2772 3175 9.699410 AATTTATCAATCCATGAAAGGTGTAGA 57.301 29.630 0.00 0.00 42.54 2.59
2773 3176 9.699410 ATTTATCAATCCATGAAAGGTGTAGAA 57.301 29.630 0.00 0.00 42.54 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.348775 CCTCCCCTCCTTCCATCCAC 61.349 65.000 0.00 0.00 0.00 4.02
1 2 1.004758 CCTCCCCTCCTTCCATCCA 59.995 63.158 0.00 0.00 0.00 3.41
2 3 2.456443 GCCTCCCCTCCTTCCATCC 61.456 68.421 0.00 0.00 0.00 3.51
3 4 1.694169 TGCCTCCCCTCCTTCCATC 60.694 63.158 0.00 0.00 0.00 3.51
4 5 2.003548 GTGCCTCCCCTCCTTCCAT 61.004 63.158 0.00 0.00 0.00 3.41
5 6 2.610859 GTGCCTCCCCTCCTTCCA 60.611 66.667 0.00 0.00 0.00 3.53
6 7 1.988982 GATGTGCCTCCCCTCCTTCC 61.989 65.000 0.00 0.00 0.00 3.46
7 8 1.274703 TGATGTGCCTCCCCTCCTTC 61.275 60.000 0.00 0.00 0.00 3.46
8 9 0.625683 ATGATGTGCCTCCCCTCCTT 60.626 55.000 0.00 0.00 0.00 3.36
9 10 1.005289 ATGATGTGCCTCCCCTCCT 59.995 57.895 0.00 0.00 0.00 3.69
10 11 1.059006 AGATGATGTGCCTCCCCTCC 61.059 60.000 0.00 0.00 0.00 4.30
11 12 0.396060 GAGATGATGTGCCTCCCCTC 59.604 60.000 0.00 0.00 0.00 4.30
12 13 1.406065 CGAGATGATGTGCCTCCCCT 61.406 60.000 0.00 0.00 0.00 4.79
13 14 1.070445 CGAGATGATGTGCCTCCCC 59.930 63.158 0.00 0.00 0.00 4.81
14 15 1.596477 GCGAGATGATGTGCCTCCC 60.596 63.158 0.00 0.00 0.00 4.30
15 16 1.596477 GGCGAGATGATGTGCCTCC 60.596 63.158 0.00 0.00 44.16 4.30
16 17 4.040068 GGCGAGATGATGTGCCTC 57.960 61.111 0.00 0.00 44.16 4.70
19 20 0.103755 TCTCTGGCGAGATGATGTGC 59.896 55.000 0.00 0.00 41.26 4.57
20 21 1.269673 CCTCTCTGGCGAGATGATGTG 60.270 57.143 0.00 0.00 44.86 3.21
21 22 1.039068 CCTCTCTGGCGAGATGATGT 58.961 55.000 0.00 0.00 44.86 3.06
22 23 1.270274 CTCCTCTCTGGCGAGATGATG 59.730 57.143 0.00 0.00 44.86 3.07
23 24 1.619654 CTCCTCTCTGGCGAGATGAT 58.380 55.000 0.00 0.00 44.86 2.45
24 25 0.467106 CCTCCTCTCTGGCGAGATGA 60.467 60.000 0.00 10.35 44.86 2.92
25 26 0.754957 ACCTCCTCTCTGGCGAGATG 60.755 60.000 0.00 7.21 44.86 2.90
26 27 0.847373 TACCTCCTCTCTGGCGAGAT 59.153 55.000 0.00 0.00 44.86 2.75
27 28 0.181587 CTACCTCCTCTCTGGCGAGA 59.818 60.000 0.00 0.00 43.82 4.04
28 29 0.181587 TCTACCTCCTCTCTGGCGAG 59.818 60.000 0.00 0.00 38.67 5.03
29 30 0.847373 ATCTACCTCCTCTCTGGCGA 59.153 55.000 0.00 0.00 35.26 5.54
30 31 1.243902 GATCTACCTCCTCTCTGGCG 58.756 60.000 0.00 0.00 35.26 5.69
31 32 1.243902 CGATCTACCTCCTCTCTGGC 58.756 60.000 0.00 0.00 35.26 4.85
32 33 1.904287 CCGATCTACCTCCTCTCTGG 58.096 60.000 0.00 0.00 37.10 3.86
33 34 1.243902 GCCGATCTACCTCCTCTCTG 58.756 60.000 0.00 0.00 0.00 3.35
34 35 0.847373 TGCCGATCTACCTCCTCTCT 59.153 55.000 0.00 0.00 0.00 3.10
35 36 0.955905 GTGCCGATCTACCTCCTCTC 59.044 60.000 0.00 0.00 0.00 3.20
36 37 0.553819 AGTGCCGATCTACCTCCTCT 59.446 55.000 0.00 0.00 0.00 3.69
37 38 0.671251 CAGTGCCGATCTACCTCCTC 59.329 60.000 0.00 0.00 0.00 3.71
38 39 0.259065 TCAGTGCCGATCTACCTCCT 59.741 55.000 0.00 0.00 0.00 3.69
39 40 0.386113 GTCAGTGCCGATCTACCTCC 59.614 60.000 0.00 0.00 0.00 4.30
40 41 1.103803 TGTCAGTGCCGATCTACCTC 58.896 55.000 0.00 0.00 0.00 3.85
41 42 0.818296 GTGTCAGTGCCGATCTACCT 59.182 55.000 0.00 0.00 0.00 3.08
42 43 0.818296 AGTGTCAGTGCCGATCTACC 59.182 55.000 0.00 0.00 0.00 3.18
43 44 2.223525 GGTAGTGTCAGTGCCGATCTAC 60.224 54.545 0.00 0.00 0.00 2.59
44 45 2.022195 GGTAGTGTCAGTGCCGATCTA 58.978 52.381 0.00 0.00 0.00 1.98
45 46 0.818296 GGTAGTGTCAGTGCCGATCT 59.182 55.000 0.00 0.00 0.00 2.75
46 47 0.818296 AGGTAGTGTCAGTGCCGATC 59.182 55.000 8.94 0.00 0.00 3.69
47 48 0.818296 GAGGTAGTGTCAGTGCCGAT 59.182 55.000 8.94 0.00 0.00 4.18
48 49 1.248785 GGAGGTAGTGTCAGTGCCGA 61.249 60.000 8.94 0.00 0.00 5.54
49 50 1.215647 GGAGGTAGTGTCAGTGCCG 59.784 63.158 8.94 0.00 0.00 5.69
50 51 1.215647 CGGAGGTAGTGTCAGTGCC 59.784 63.158 6.69 6.69 0.00 5.01
51 52 0.388649 CACGGAGGTAGTGTCAGTGC 60.389 60.000 0.00 0.00 34.15 4.40
52 53 0.243907 CCACGGAGGTAGTGTCAGTG 59.756 60.000 0.00 0.00 39.14 3.66
53 54 0.898789 CCCACGGAGGTAGTGTCAGT 60.899 60.000 0.00 0.00 37.88 3.41
54 55 0.611062 TCCCACGGAGGTAGTGTCAG 60.611 60.000 0.00 0.00 37.88 3.51
55 56 0.611062 CTCCCACGGAGGTAGTGTCA 60.611 60.000 0.00 0.00 45.43 3.58
56 57 2.190756 CTCCCACGGAGGTAGTGTC 58.809 63.158 0.00 0.00 45.43 3.67
57 58 4.436368 CTCCCACGGAGGTAGTGT 57.564 61.111 0.00 0.00 45.43 3.55
65 66 4.075793 CTCCCTCCCTCCCACGGA 62.076 72.222 0.00 0.00 0.00 4.69
67 68 3.618855 TTCCTCCCTCCCTCCCACG 62.619 68.421 0.00 0.00 0.00 4.94
68 69 1.690985 CTTCCTCCCTCCCTCCCAC 60.691 68.421 0.00 0.00 0.00 4.61
69 70 2.787866 CTTCCTCCCTCCCTCCCA 59.212 66.667 0.00 0.00 0.00 4.37
70 71 2.040359 CCTTCCTCCCTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
71 72 0.692756 CTTCCTTCCTCCCTCCCTCC 60.693 65.000 0.00 0.00 0.00 4.30
72 73 0.340208 TCTTCCTTCCTCCCTCCCTC 59.660 60.000 0.00 0.00 0.00 4.30
73 74 0.800239 TTCTTCCTTCCTCCCTCCCT 59.200 55.000 0.00 0.00 0.00 4.20
74 75 1.670059 TTTCTTCCTTCCTCCCTCCC 58.330 55.000 0.00 0.00 0.00 4.30
75 76 2.615747 CGTTTTCTTCCTTCCTCCCTCC 60.616 54.545 0.00 0.00 0.00 4.30
76 77 2.038689 ACGTTTTCTTCCTTCCTCCCTC 59.961 50.000 0.00 0.00 0.00 4.30
77 78 2.055579 ACGTTTTCTTCCTTCCTCCCT 58.944 47.619 0.00 0.00 0.00 4.20
78 79 2.563261 ACGTTTTCTTCCTTCCTCCC 57.437 50.000 0.00 0.00 0.00 4.30
79 80 4.454847 CCTAAACGTTTTCTTCCTTCCTCC 59.545 45.833 20.19 0.00 0.00 4.30
80 81 5.178996 GTCCTAAACGTTTTCTTCCTTCCTC 59.821 44.000 20.19 0.00 0.00 3.71
81 82 5.061853 GTCCTAAACGTTTTCTTCCTTCCT 58.938 41.667 20.19 0.00 0.00 3.36
82 83 4.084171 CGTCCTAAACGTTTTCTTCCTTCC 60.084 45.833 20.19 0.00 46.42 3.46
83 84 5.015067 CGTCCTAAACGTTTTCTTCCTTC 57.985 43.478 20.19 1.99 46.42 3.46
94 95 9.982808 GATCACTTGATCGATCGTCCTAAACGT 62.983 44.444 20.03 2.31 44.81 3.99
95 96 7.745018 GATCACTTGATCGATCGTCCTAAACG 61.745 46.154 20.03 1.69 45.31 3.60
96 97 4.669318 TCACTTGATCGATCGTCCTAAAC 58.331 43.478 20.03 0.00 0.00 2.01
97 98 4.976224 TCACTTGATCGATCGTCCTAAA 57.024 40.909 20.03 7.12 0.00 1.85
98 99 5.109662 GATCACTTGATCGATCGTCCTAA 57.890 43.478 20.03 7.81 41.15 2.69
99 100 4.750952 GATCACTTGATCGATCGTCCTA 57.249 45.455 20.03 6.49 41.15 2.94
100 101 3.634568 GATCACTTGATCGATCGTCCT 57.365 47.619 20.03 0.88 41.15 3.85
110 111 6.543465 TGTTTGTGTTTGAGAGATCACTTGAT 59.457 34.615 0.00 0.00 37.51 2.57
111 112 5.879777 TGTTTGTGTTTGAGAGATCACTTGA 59.120 36.000 0.00 0.00 0.00 3.02
112 113 5.967674 GTGTTTGTGTTTGAGAGATCACTTG 59.032 40.000 0.00 0.00 0.00 3.16
113 114 5.882557 AGTGTTTGTGTTTGAGAGATCACTT 59.117 36.000 0.00 0.00 0.00 3.16
114 115 5.431765 AGTGTTTGTGTTTGAGAGATCACT 58.568 37.500 0.00 0.00 0.00 3.41
115 116 5.741388 AGTGTTTGTGTTTGAGAGATCAC 57.259 39.130 0.00 0.00 0.00 3.06
116 117 5.296780 GGAAGTGTTTGTGTTTGAGAGATCA 59.703 40.000 0.00 0.00 0.00 2.92
117 118 5.296780 TGGAAGTGTTTGTGTTTGAGAGATC 59.703 40.000 0.00 0.00 0.00 2.75
118 119 5.192927 TGGAAGTGTTTGTGTTTGAGAGAT 58.807 37.500 0.00 0.00 0.00 2.75
119 120 4.584874 TGGAAGTGTTTGTGTTTGAGAGA 58.415 39.130 0.00 0.00 0.00 3.10
120 121 4.963276 TGGAAGTGTTTGTGTTTGAGAG 57.037 40.909 0.00 0.00 0.00 3.20
121 122 4.157656 CCTTGGAAGTGTTTGTGTTTGAGA 59.842 41.667 0.00 0.00 0.00 3.27
122 123 4.423732 CCTTGGAAGTGTTTGTGTTTGAG 58.576 43.478 0.00 0.00 0.00 3.02
123 124 3.194542 CCCTTGGAAGTGTTTGTGTTTGA 59.805 43.478 0.00 0.00 0.00 2.69
124 125 3.520569 CCCTTGGAAGTGTTTGTGTTTG 58.479 45.455 0.00 0.00 0.00 2.93
125 126 2.499693 CCCCTTGGAAGTGTTTGTGTTT 59.500 45.455 0.00 0.00 0.00 2.83
126 127 2.107366 CCCCTTGGAAGTGTTTGTGTT 58.893 47.619 0.00 0.00 0.00 3.32
127 128 1.006639 ACCCCTTGGAAGTGTTTGTGT 59.993 47.619 0.00 0.00 34.81 3.72
128 129 1.775385 ACCCCTTGGAAGTGTTTGTG 58.225 50.000 0.00 0.00 34.81 3.33
129 130 3.895704 ATACCCCTTGGAAGTGTTTGT 57.104 42.857 0.00 0.00 34.81 2.83
130 131 5.185056 CCTTTATACCCCTTGGAAGTGTTTG 59.815 44.000 0.00 0.00 34.81 2.93
131 132 5.162914 ACCTTTATACCCCTTGGAAGTGTTT 60.163 40.000 0.00 0.00 34.81 2.83
132 133 4.355889 ACCTTTATACCCCTTGGAAGTGTT 59.644 41.667 0.00 0.00 34.81 3.32
133 134 3.920841 ACCTTTATACCCCTTGGAAGTGT 59.079 43.478 0.00 0.00 34.81 3.55
134 135 4.586306 ACCTTTATACCCCTTGGAAGTG 57.414 45.455 0.00 0.00 34.81 3.16
135 136 5.974370 TCATACCTTTATACCCCTTGGAAGT 59.026 40.000 0.00 0.00 34.81 3.01
136 137 6.509523 TCATACCTTTATACCCCTTGGAAG 57.490 41.667 0.00 0.00 34.81 3.46
137 138 7.474474 AATCATACCTTTATACCCCTTGGAA 57.526 36.000 0.00 0.00 34.81 3.53
138 139 7.474474 AAATCATACCTTTATACCCCTTGGA 57.526 36.000 0.00 0.00 34.81 3.53
139 140 8.547481 AAAAATCATACCTTTATACCCCTTGG 57.453 34.615 0.00 0.00 37.80 3.61
140 141 9.196139 TGAAAAATCATACCTTTATACCCCTTG 57.804 33.333 0.00 0.00 0.00 3.61
141 142 9.421399 CTGAAAAATCATACCTTTATACCCCTT 57.579 33.333 0.00 0.00 0.00 3.95
142 143 8.004801 CCTGAAAAATCATACCTTTATACCCCT 58.995 37.037 0.00 0.00 0.00 4.79
143 144 8.002459 TCCTGAAAAATCATACCTTTATACCCC 58.998 37.037 0.00 0.00 0.00 4.95
144 145 8.990163 TCCTGAAAAATCATACCTTTATACCC 57.010 34.615 0.00 0.00 0.00 3.69
163 164 9.787532 CGCTTAAAGAATATGAAAATTCCTGAA 57.212 29.630 0.00 0.00 36.68 3.02
164 165 9.173021 TCGCTTAAAGAATATGAAAATTCCTGA 57.827 29.630 0.00 0.00 36.68 3.86
165 166 9.443283 CTCGCTTAAAGAATATGAAAATTCCTG 57.557 33.333 0.00 0.00 36.68 3.86
166 167 9.396022 TCTCGCTTAAAGAATATGAAAATTCCT 57.604 29.630 0.00 0.00 36.68 3.36
170 171 9.941664 CACATCTCGCTTAAAGAATATGAAAAT 57.058 29.630 0.00 0.00 0.00 1.82
171 172 8.946085 ACACATCTCGCTTAAAGAATATGAAAA 58.054 29.630 0.00 0.00 0.00 2.29
172 173 8.492673 ACACATCTCGCTTAAAGAATATGAAA 57.507 30.769 0.00 0.00 0.00 2.69
173 174 7.763985 TGACACATCTCGCTTAAAGAATATGAA 59.236 33.333 0.00 0.00 0.00 2.57
182 183 9.841880 GATATATACTGACACATCTCGCTTAAA 57.158 33.333 0.00 0.00 0.00 1.52
183 184 9.010029 TGATATATACTGACACATCTCGCTTAA 57.990 33.333 0.00 0.00 0.00 1.85
187 188 6.612306 TGTGATATATACTGACACATCTCGC 58.388 40.000 0.00 0.00 36.72 5.03
252 253 8.893727 AGCACTTATATCTCAATAAAAACGCTT 58.106 29.630 0.00 0.00 0.00 4.68
270 271 9.938280 TCAAAACAGTATTGTACTAGCACTTAT 57.062 29.630 0.00 0.00 37.23 1.73
271 272 9.938280 ATCAAAACAGTATTGTACTAGCACTTA 57.062 29.630 0.00 0.00 37.23 2.24
274 275 9.582431 TCTATCAAAACAGTATTGTACTAGCAC 57.418 33.333 0.00 0.00 37.23 4.40
287 288 4.960938 TGCAGTGAGTCTATCAAAACAGT 58.039 39.130 0.00 0.00 40.43 3.55
288 289 5.929697 TTGCAGTGAGTCTATCAAAACAG 57.070 39.130 0.00 0.00 40.43 3.16
289 290 5.822519 AGTTTGCAGTGAGTCTATCAAAACA 59.177 36.000 0.00 0.00 40.43 2.83
290 291 6.138761 CAGTTTGCAGTGAGTCTATCAAAAC 58.861 40.000 0.00 0.00 40.43 2.43
293 294 3.748048 GCAGTTTGCAGTGAGTCTATCAA 59.252 43.478 0.00 0.00 44.26 2.57
294 295 3.329386 GCAGTTTGCAGTGAGTCTATCA 58.671 45.455 0.00 0.00 44.26 2.15
337 338 2.610694 CCTCTGCAACACCAGCACG 61.611 63.158 0.00 0.00 37.02 5.34
346 347 2.505364 ATTCAGGGGCCCTCTGCAAC 62.505 60.000 26.02 9.30 43.89 4.17
401 402 2.625823 GGGCGTGCTTAGCTTTGCA 61.626 57.895 5.60 8.90 36.79 4.08
412 413 3.075005 TCCTAGGAGTGGGCGTGC 61.075 66.667 7.62 0.00 0.00 5.34
413 414 1.541310 TTGTCCTAGGAGTGGGCGTG 61.541 60.000 13.15 0.00 30.50 5.34
426 427 0.846693 AACTGTTGCCTCCTTGTCCT 59.153 50.000 0.00 0.00 0.00 3.85
427 428 1.239347 GAACTGTTGCCTCCTTGTCC 58.761 55.000 0.00 0.00 0.00 4.02
433 434 3.674997 TGATTACTGAACTGTTGCCTCC 58.325 45.455 0.00 0.00 0.00 4.30
440 442 7.901029 TCTCTCTGAAATGATTACTGAACTGT 58.099 34.615 0.00 0.00 0.00 3.55
448 450 7.148188 TGGCATTGTTCTCTCTGAAATGATTAC 60.148 37.037 2.55 0.00 36.30 1.89
477 479 2.287487 TGTTGGATGTGCATGTGTTTCG 60.287 45.455 0.00 0.00 0.00 3.46
504 506 4.600692 ACTCCTGTGCCCATTTTAAAAC 57.399 40.909 1.97 0.00 0.00 2.43
548 572 9.730705 TCTACTTTAGCTACTACTAACAGACAA 57.269 33.333 0.00 0.00 31.94 3.18
549 573 9.730705 TTCTACTTTAGCTACTACTAACAGACA 57.269 33.333 0.00 0.00 31.94 3.41
551 575 8.891720 GCTTCTACTTTAGCTACTACTAACAGA 58.108 37.037 0.00 0.00 31.94 3.41
552 576 8.675504 TGCTTCTACTTTAGCTACTACTAACAG 58.324 37.037 0.00 0.00 38.22 3.16
553 577 8.571461 TGCTTCTACTTTAGCTACTACTAACA 57.429 34.615 0.00 0.00 38.22 2.41
554 578 9.852091 TTTGCTTCTACTTTAGCTACTACTAAC 57.148 33.333 0.00 0.00 38.22 2.34
556 580 8.189460 GCTTTGCTTCTACTTTAGCTACTACTA 58.811 37.037 0.00 0.00 38.22 1.82
557 581 7.036829 GCTTTGCTTCTACTTTAGCTACTACT 58.963 38.462 0.00 0.00 38.22 2.57
558 582 6.020520 CGCTTTGCTTCTACTTTAGCTACTAC 60.021 42.308 0.00 0.00 38.22 2.73
559 583 6.034591 CGCTTTGCTTCTACTTTAGCTACTA 58.965 40.000 0.00 0.00 38.22 1.82
564 588 3.484393 GCTCGCTTTGCTTCTACTTTAGC 60.484 47.826 0.00 0.00 37.89 3.09
642 669 5.596836 TTGATCAGCACTTGGTTCTTTTT 57.403 34.783 0.00 0.00 0.00 1.94
643 670 5.596836 TTTGATCAGCACTTGGTTCTTTT 57.403 34.783 0.00 0.00 0.00 2.27
644 671 5.596836 TTTTGATCAGCACTTGGTTCTTT 57.403 34.783 0.00 0.00 0.00 2.52
645 672 5.596836 TTTTTGATCAGCACTTGGTTCTT 57.403 34.783 0.00 0.00 0.00 2.52
693 720 2.237751 CGAGGCGGAATAGCAACGG 61.238 63.158 0.00 0.00 39.27 4.44
744 771 0.391793 GCTTCTGGGAAGGACCGAAG 60.392 60.000 8.98 0.00 40.66 3.79
745 772 0.836400 AGCTTCTGGGAAGGACCGAA 60.836 55.000 8.98 0.00 40.11 4.30
746 773 1.229209 AGCTTCTGGGAAGGACCGA 60.229 57.895 8.98 0.00 40.11 4.69
747 774 1.078848 CAGCTTCTGGGAAGGACCG 60.079 63.158 8.98 0.00 40.11 4.79
748 775 1.377856 GCAGCTTCTGGGAAGGACC 60.378 63.158 8.98 0.00 38.08 4.46
749 776 1.377856 GGCAGCTTCTGGGAAGGAC 60.378 63.158 8.98 0.00 31.21 3.85
806 833 1.336887 GGGCTATTTATGCTCGCTCGA 60.337 52.381 0.00 0.00 0.00 4.04
861 888 0.178987 GGGAGTCGGATGCTAGGAGA 60.179 60.000 0.00 0.00 0.00 3.71
866 893 1.152525 GGGAGGGAGTCGGATGCTA 60.153 63.158 0.00 0.00 0.00 3.49
906 966 1.060779 CGCTGTGTGTGTGTGTGTG 59.939 57.895 0.00 0.00 0.00 3.82
907 967 2.749865 GCGCTGTGTGTGTGTGTGT 61.750 57.895 0.00 0.00 0.00 3.72
908 968 2.023181 GCGCTGTGTGTGTGTGTG 59.977 61.111 0.00 0.00 0.00 3.82
909 969 3.563088 CGCGCTGTGTGTGTGTGT 61.563 61.111 5.56 0.00 32.50 3.72
910 970 3.214306 CTCGCGCTGTGTGTGTGTG 62.214 63.158 5.56 0.00 37.85 3.82
911 971 2.961721 CTCGCGCTGTGTGTGTGT 60.962 61.111 5.56 0.00 37.85 3.72
912 972 4.360027 GCTCGCGCTGTGTGTGTG 62.360 66.667 5.56 0.00 37.97 3.82
1083 1158 3.457263 TGGCCGTGCTGCTCGATA 61.457 61.111 23.74 8.00 0.00 2.92
1213 1288 1.556911 GATGGCTTCTTCCTCCTCACA 59.443 52.381 0.00 0.00 0.00 3.58
1215 1290 1.956869 TGATGGCTTCTTCCTCCTCA 58.043 50.000 1.86 0.00 0.00 3.86
1252 1327 0.392998 GTGGACCATCTGTTGCCGAT 60.393 55.000 0.00 0.00 0.00 4.18
1575 1674 1.472878 TCGTCAATCTGGAACTCCTCG 59.527 52.381 0.00 0.00 36.82 4.63
1816 1996 3.313249 TCAGTCGACGAACTACAGAAACA 59.687 43.478 10.46 0.00 0.00 2.83
1834 2040 1.212935 AGCAACAAGGGTCAACTCAGT 59.787 47.619 0.00 0.00 0.00 3.41
1890 2097 1.009829 CGCCCGGAGAAAATTCTGAG 58.990 55.000 0.73 0.00 37.73 3.35
1891 2098 0.323629 ACGCCCGGAGAAAATTCTGA 59.676 50.000 0.73 0.00 37.73 3.27
1892 2099 0.447801 CACGCCCGGAGAAAATTCTG 59.552 55.000 0.73 0.00 37.73 3.02
2016 2228 7.524367 CGAAGAAAGGGTTCAGTAAGGTTACTA 60.524 40.741 2.06 0.00 41.82 1.82
2029 2245 1.535896 GGAGCAACGAAGAAAGGGTTC 59.464 52.381 0.00 0.00 0.00 3.62
2060 2276 4.399303 AGCAGCGCTCTTTGGTATTTTTAT 59.601 37.500 7.13 0.00 30.62 1.40
2098 2314 2.103042 GGATCGGACAGCTGTGCAC 61.103 63.158 33.52 23.55 36.05 4.57
2107 2323 4.492160 GCGCAGACGGATCGGACA 62.492 66.667 0.30 0.00 40.57 4.02
2120 2520 1.521457 GATCGAAGGGTCATGCGCA 60.521 57.895 14.96 14.96 0.00 6.09
2236 2636 3.941188 CGGTGGTGCAGGGTGACT 61.941 66.667 0.00 0.00 0.00 3.41
2240 2640 3.352990 AACAACGGTGGTGCAGGGT 62.353 57.895 4.97 0.00 0.00 4.34
2244 2644 0.466543 AGTAGAACAACGGTGGTGCA 59.533 50.000 4.97 0.00 0.00 4.57
2250 2650 1.067071 GCTGGCTAGTAGAACAACGGT 60.067 52.381 0.00 0.00 0.00 4.83
2272 2672 1.421410 CCGTTGAGGTGCTACGATGC 61.421 60.000 0.00 0.00 46.30 3.91
2315 2716 2.476185 GCTGGCGACAATACAACATCAC 60.476 50.000 0.00 0.00 42.06 3.06
2346 2747 1.868251 CTTCCGACGACGCTGCTAC 60.868 63.158 0.64 0.00 38.29 3.58
2407 2808 4.100084 CCTCGTGATGGGGCTGCA 62.100 66.667 0.50 0.00 0.00 4.41
2416 2817 1.404391 CTACGGTGCTAACCTCGTGAT 59.596 52.381 0.00 0.00 45.17 3.06
2420 2821 0.801067 GTGCTACGGTGCTAACCTCG 60.801 60.000 3.74 0.00 45.17 4.63
2421 2822 0.531200 AGTGCTACGGTGCTAACCTC 59.469 55.000 3.74 0.00 45.17 3.85
2423 2824 0.739813 CCAGTGCTACGGTGCTAACC 60.740 60.000 3.74 0.00 43.76 2.85
2424 2825 0.037605 ACCAGTGCTACGGTGCTAAC 60.038 55.000 3.74 0.00 33.05 2.34
2425 2826 0.037697 CACCAGTGCTACGGTGCTAA 60.038 55.000 6.14 0.00 45.77 3.09
2426 2827 1.589630 CACCAGTGCTACGGTGCTA 59.410 57.895 6.14 0.00 45.77 3.49
2427 2828 2.343758 CACCAGTGCTACGGTGCT 59.656 61.111 6.14 0.00 45.77 4.40
2439 2840 1.613630 ACCTGTAGGGGAGCACCAG 60.614 63.158 1.58 0.00 42.91 4.00
2440 2841 1.612442 GACCTGTAGGGGAGCACCA 60.612 63.158 1.58 0.00 42.91 4.17
2460 2861 0.820891 CTTCAAGATGGATGGGGGCG 60.821 60.000 0.00 0.00 0.00 6.13
2461 2862 1.111715 GCTTCAAGATGGATGGGGGC 61.112 60.000 0.00 0.00 0.00 5.80
2462 2863 0.259647 TGCTTCAAGATGGATGGGGG 59.740 55.000 0.00 0.00 0.00 5.40
2463 2864 1.396653 GTGCTTCAAGATGGATGGGG 58.603 55.000 0.00 0.00 0.00 4.96
2483 2884 2.125512 ACTCGCCCGACATTGCTC 60.126 61.111 0.00 0.00 0.00 4.26
2485 2886 4.166011 GCACTCGCCCGACATTGC 62.166 66.667 0.00 0.00 0.00 3.56
2527 2929 1.671742 GGACGGAGAGCCACAAGAA 59.328 57.895 0.00 0.00 0.00 2.52
2528 2930 2.636412 CGGACGGAGAGCCACAAGA 61.636 63.158 0.00 0.00 0.00 3.02
2529 2931 2.125912 CGGACGGAGAGCCACAAG 60.126 66.667 0.00 0.00 0.00 3.16
2534 2936 2.182030 CAAGTCGGACGGAGAGCC 59.818 66.667 1.89 0.00 0.00 4.70
2537 2939 2.962569 CTGCAAGTCGGACGGAGA 59.037 61.111 1.89 0.00 0.00 3.71
2571 2974 4.354212 CGGCACTGCGACACAACG 62.354 66.667 0.00 0.00 0.00 4.10
2599 3002 3.667282 GCTGCTATGCCATGCCCG 61.667 66.667 0.00 0.00 0.00 6.13
2603 3006 3.028130 CGGTGCTGCTATGCCATG 58.972 61.111 0.00 0.00 0.00 3.66
2604 3007 2.903855 GCGGTGCTGCTATGCCAT 60.904 61.111 0.00 0.00 0.00 4.40
2619 3022 4.114997 GGGATGGTTGTTGCCGCG 62.115 66.667 0.00 0.00 0.00 6.46
2663 3066 9.713713 GGCCCAACAAAGTCTATAAAAATAAAA 57.286 29.630 0.00 0.00 0.00 1.52
2666 3069 7.340999 GGAGGCCCAACAAAGTCTATAAAAATA 59.659 37.037 0.00 0.00 0.00 1.40
2667 3070 6.154534 GGAGGCCCAACAAAGTCTATAAAAAT 59.845 38.462 0.00 0.00 0.00 1.82
2668 3071 5.479027 GGAGGCCCAACAAAGTCTATAAAAA 59.521 40.000 0.00 0.00 0.00 1.94
2669 3072 5.014202 GGAGGCCCAACAAAGTCTATAAAA 58.986 41.667 0.00 0.00 0.00 1.52
2670 3073 4.043561 TGGAGGCCCAACAAAGTCTATAAA 59.956 41.667 0.00 0.00 40.09 1.40
2673 3076 1.992557 TGGAGGCCCAACAAAGTCTAT 59.007 47.619 0.00 0.00 40.09 1.98
2674 3077 1.440618 TGGAGGCCCAACAAAGTCTA 58.559 50.000 0.00 0.00 40.09 2.59
2675 3078 0.555769 TTGGAGGCCCAACAAAGTCT 59.444 50.000 0.00 0.00 46.94 3.24
2676 3079 0.961753 CTTGGAGGCCCAACAAAGTC 59.038 55.000 0.00 0.00 46.94 3.01
2677 3080 0.261696 ACTTGGAGGCCCAACAAAGT 59.738 50.000 0.00 4.01 46.94 2.66
2678 3081 2.286365 TACTTGGAGGCCCAACAAAG 57.714 50.000 0.00 3.30 46.94 2.77
2679 3082 2.990740 ATACTTGGAGGCCCAACAAA 57.009 45.000 0.00 0.00 46.94 2.83
2680 3083 3.186283 TCTATACTTGGAGGCCCAACAA 58.814 45.455 0.00 1.03 46.94 2.83
2716 3119 9.578439 GGTCATCCTTTTGAGAGAAATTTATTG 57.422 33.333 0.00 0.00 0.00 1.90


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.